Peichuan Zhang Answered Feb 17, 2012
Department of Biology, The Pennsylvania State University, USA
Hi Sophia,
Thanks! I'm glad that our protocols have attracted attention from potential users.
We have been using regular agarose gel (2.0%) and 1X TAE buffer all the time. In my case, I need to separate two bands of about 200-bp (with difference of ~30-bp), and sometimes, I used 2.5% agarose gel instead. Try to not use too high voltage to avoid "smiling effects", and always remember to have positive and negative controls for comparison. Also use fresh 1X TAE buffer, as its buffering capacity drops significantly after a few rounds. You may consider designing a few different PCR-restriction digest strategies and pick the one that produces best resolution.
I only used TBE buffer, which is better than TAE in its buffering capacity, for gel shifting experiments. I recall that I saw some notes about achieving better resolution with TBE for smaller DNA (<300-bp on 2% agarose gel).
Hope this would help you a bit. Please let me know if you have further questions, and best luck with your experiments.
Peichuan